After arriving to Iconia, the Yamato received an Iconian software transmission and was unable to continue the investigation due to random system failures, later on discovered to have been caused by the software. An engineering team of 18 was killed when the the force field in a shuttle bay was shut down. The Yamato left Iconia to rendezvous with the Enterprise-D to solve the malfunctions and convince Captain Jean-Luc Picard to continue with the exploration of Iconia. The IRW Haakona under cloak detected the Yamato and copied its log transmissions to the Enterprise-D, while it was traveling to the rendezvous.

After the Yamato had arrived closer to the Federation side of the Neutral Zone, a position twelve hours and sixteen minutes away from Iconia at warp 8. The Iconian software caused an antimatter containment failure. The magnetic seals around the dilithium chamber collapsed, and the computer initiated the emergency release system to dump the Yamato's supply of antimatter. However, the program caused the release to halt with antimatter remaining within the ship, resulting in a warp core breach. The Yamato was lost with all hands. (TNG: "Contagion")

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↑ The Yamato's registry was identified by dialog in "Where Silence Has Lease" by Riker who visually identified it from the hull of Nagilum's reproduction and stated it to be NCC-1305-E. But the later appearance in "Contagion", the physical saucer model of the Yamato and several computer screens, schematics and captain's logs identified the registry as NCC-71807. As both registries are canon, and as prominent, we assume the registry of the Yamato was simply redesignated in early 2365.

According to Star Trek Encyclopedia (3ed. p.569), the initial registry number was a production mistake. It was given to the Yamato by the episode writer Jack B. Sowards who was unaware of the registry numbering scheme developed for Star Trek: The Next Generation. Michael Okuda had intended to correct the number to NCC-71807 as he had already finished the decals for the saucer section of the the model for "Contagion" with that number, but as the scene was removed from an intermediate draft, he dropped the issue, only to find out the scene had been re-added later on to the final draft, which Okuda realized after the episode had aired.

Star Trek Encyclopedia states that the Yamato was named after the battleship Yamato, which served as flagship of the Imperial Japanese Navy during World War II. According to technical illustrator and modeler Rick Sternbach, the name was not a reference to the Japanese anime series Space Battleship Yamato (or Star Blazers in North America), even though he and several other members of the production staff are fans of Japanese animation. Sternbach stated at AnimeCon 1991 that the TNG writers had independently coined the ship's name without his input and he doubts that the writers were aware of the anime connection.

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